In 1932 the New York Harlem Stars became the New York Black Yankees. An independent team under the management of 2B Tubby Scales (.292), the Black Yankees went 14-11 against other top black teams in their first season. OF Crush Holloway hit .364 while Bill Holland (6-1) and Connie Rector (6-2) led the staff. In 1933 they were just 1-6 against other top black teams, though Scales hit .375, 2B Rev Cannady batted .364 and 3B John Beckwith hit .391. The Black Yankees were 2-10 in 1934 with Holland dropping all 4 of his decisions. Beckwith fell to .286, Scales to .200 and Cannady to .190 while Fats Jenkins hit .333. They were 11-6 in 1936 as Bob Clark and Ramiro Ramirez managed the team. Scales hit .358 as Jenkins slipped to .209. Holland bounced back to go 7-2.

The Black Yankees joined the Negro National League in 1937 and finished last at 9-14. Clark managed the club, for which Cannady hit .365 and OF Marvin Barker .410. Cannady became manager in 1938 while batting .179. Only 2B Dave Campbell topped .300 as the club went 7-18. They improved to 15-21 in 1939 with OF Goose Curry (.352) the sole player over .285. Terris McDuffie went 5-3 and Holland was 4-2. Back in last in 1940, the Black Yankees were managed by Tex Burnett and led by 2B Flash Miller (.455). They moved up to fifth in the six-team league in 1941 though Burnett's team had three players at or below the Mendoza Line. Satchel Paige, on loan from the Kansas City Monarchs, made his first comeback appearance after recovering from his arm injury, pitching for the Black Yankees in their opener that season, getting a victory.

Before the beginning of the 1942 season, the Yankees merged with the St. Louis Stars of the NAL and acquired the Stars' best players. The NAL protested that the players' contracts reverted to the league when the Stars dropped out of the NAL, but the Yankees kept the players despite the protests. In retaliation, the NAL voted to boycott the Black Yankees and prohibit their members from playing any interleague games with them. This cost the Yankees a few potentially lucrative pre-season matchups, but the boycott ended when they played against the Birmingham Black Barons in an interleague exhibition game in St. Louis on May 30.

Despite the merger, the team fell back to last at 8-18 in 1942, reversing spots with the equally pitiful New York Cubans. 2B Dick Seay hit .364. They lost all 8 games in 1943 and 24 of 28 games in 1944 with Scales back at the helm. SS Willie Wells hit .500 in limited time while OF Thad Christopher batted .386. They remained in the cellar in 1945 at 7-26 and Bill Perkins replaced Scales at the helm. Wells slipped to .280, still one of the team's better bats, and Barker hit .353. They did even worse in 1946, with an 8-40 mark. Wells hit .278, though Seay batted just .143. Bill Ricks posted an 0-10 record on the mound.

The New York, NY team "improved" to 8-33 in 1947 and they did their usual last-place finish in their final NNL season in New York City, having never finished over .500 as a league member. The team introduced future big-leaguer George Crowe at first base.

In 1948, the New York Black Yankees relocated to Red Wing Stadium in Rochester, NY for what would become their final season. Despite featuring the talents of the aformentioned Crowe, and with future Hall-of-Famer Mule Suttles on their coaching staff, they finished 8-32 in league play, and officially disbanded in September.

However, over the next 57 years, the Black Yankees move to Rochester would lost to history, as every reference material published would inaccurately continue to list Yankee Stadium as their home for that final season. This mistake was likely due to a combination of three factors; most notably the team kept the name "New York Black Yankees" (presumably the "New York" would now represent the state in which the team was located), the team also folded before the end of the season and the whole league folded at the conclusion of the season. In 2005, Douglas Brei, a Rochester-native, discovered the teams ties to Rochester, and after providing his research to the editors of the Baseball Encyclopedia a modification was made in the 2006 edition to recognize Rochester as the Black Yankees' final home.